Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra�ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota. There were four major habitat types (rubble/rock, sand/coral matrix, algal rim and sand) identified, the most extensive being rubble/rock (45%) and sand/coral matrix (35%). The degree of exposure to winds was found to correlate with the reef development and habitat distribution. The assemblage composition of each major habitat type differed significantly from every other habitat. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity, and the highest number of species and individuals. The overall abundance of the fauna was dominated by holothurians (68%) and echinoids (30%), while Trochus niloticus and Tridacna maxima accounted for the remaining 2% of the total invertebrate assemblage. Clear habitat partitioning was also found for adult and juvenile Trochus niloticus and Tridacna maxima. In the traditional fishery for Holothuria leucospilota, the mature gonads of males are harvested by making an incision in the body-wall of the animal, removing the gonads and then returning the animal to the reef to allow regeneration. Monthly collections of H. leucospilota were used to describe the reproductive biology of this species. Gametogenesis and spawning were synchronous between the sexes and spawning occurred annually during summer, when water temperature and photoperiod were at their highest. Although the incision in the body-wall and gonad removal had no impact on the survival of H.leucospilota in experimental cages, their body weight, and general sheltering and feeding behaviors were affected. Gonads took at least 41 days to start regenerating, suggesting a considerable delay in the spawning of fished individuals. In 1998, five Rarotongan communities re-introduced the traditional ra�ui system of resource management, prohibiting all fishing and gathering from their reefs. The performance of the Nikao ra�ui, which had been put in place to allow trochus stocks to increase, was investigated. Comparisons of macroinvertebrate assemblage composition and species density were made between three fishing treatments, i.e. fished areas adjacent to the ra�ui, within the ra�ui after two years of protection, and in the ra�ui after it had been lifted for three weeks to allow a commercial trochus harvest. Analysis of variance on the count data for the twelve most abundant species, and non-metric multi-dimensional scaling indicated that there were no differences in the microhabitat or the invertebrate assemblage composition between the three fishing treatments. However, there were significant differences between the rubble/rock and sand/coral matrix habitat types. The results on the effectiveness of the Nikao ra�ui are equivocal, due to the small sample size, and the variability between samples which was highlighted by the wide confidence intervals. This study highlights the importance of habitat to the macroinvertebrate fauna of the reef-top and the need for accurate habitat maps to increase the cost-effectiveness of future resource surveys, to provide information to management, and for the design of Marine Protected Areas. The mapping and survey methods must be reliable and repeatable in terms of the limitations of time, and the availability of expertise, funding and resources. The results provide important information for fisheries and conservation managers of Rarotonga and other Pacific Islands to better design rigorous sampling programmes for monitoring the status of reef-top resources, and for evaluating and planning Marine Protected Areas.

Coral reefs are in global decline, with seaweeds increasing as corals decrease. Though seaweeds have been shown to inhibit coral growth, recruitment, and survivorship, the mechanism of these interactions is poorly known. Here we use field experiments to show that contact with four common seaweeds induces bleaching on natural colonies of Porites rus. Controls in contact with inert, plastic mimics of seaweeds did not bleach, suggesting treatment effects resulted from allelopathy rather than shading, abrasion, or physical contact. Bioassay-guided fractionation of the hydrophobic extract from the red alga Phacelocarpus neurymenioides revealed a previously characterized antibacterial metabolite, Neurymenolide A, as the main allelopathic agent. For allelopathy of lipid soluble metabolites to be effective, the metabolites would need to be deployed on algal surfaces where they could transfer to corals on contact. We used desorption electrospray ionization mass spectrometry (DESI-MS) to visualize and quantify Neurymenolide A on the surface of P. neurymenioides and found the metabolite on all surfaces analyzed. The highest concentrations of Neurymenolide A were on basal portions of blades where the plant is most likely to contact other benthic competitors.

An appreciation of the extent of syndepositional fracturing, faulting, and cementation of carbonate platform margins is essential to understanding the role of early diagenesis and compaction in margin deformation. This study uses integrated lidar and outcrop data along the Capitan Reef from an area encompassing the mouths of both Rattlesnake and Walnut Canyons. Mapping geomorphic expressions of syndepositional faults and fractures at multiple scales of observation was the main approach to delineating zones of syndepositional fractures. Ridge- groove couplets visible in exposures of the Capitan Reef throughout the Guadalupe Mountains were targeted because the ability to identify these as signs of syndepositional fracture development would have implications for the entire reef complex. Results show that these ridgegroove couplets are the product of differential weathering of syndepositional as well as burial-related fractures. Recessive grooves have an average syndepositional fracture spacing of ~13 m whereas ridges have a spacing of ~33 m. vi Smaller (~5-20 m-wide) scale erosional lineaments common in the study area and mappable on airborne lidar are formed by differential erosion of planes of syndepositional faults. Maps of these fault lineaments on the lidar show that syndepositional faults extend laterally for 300 m - 2000 m and relay near the terminations of the faults at each end. Faults can be further grouped into fault systems consisting of sets of faults connected by fault relays that extend for at least the entire length (~12 km) of the study area. Although vertical displacement along faults is typically less than 11 m, syndepositional faults result in changes in structural dip domain of 1-6 degrees across an individual fault. Even smaller erosional lineaments (10 cm-1 m) are visible on the airborne lidar that form as a result of differential erosion of individual fractures. Larger fractures (> 20 cm) can be reliably mapped on the lidar, but smaller features (< 20 cm) cannot be reliably mapped with currently available data and can only be captured using field studies. Fracture fill types are heterogeneous along strike as shown by comparisons of field study locations. Siliciclastic-dominated fills are likely sourced from overlying siliciclastic units of the shelf, which, in this area, were from the Ocotillo Siltstone. These silt-filled fractures are broadly distributed, indicating preferential development and infill of syndepositional fractures during the deposition of the Ocotillo Siltstone in the G27/28 high-frequency sequences. Development of early fractures is also shown to have been influenced by mechanical stratigraphy with changes in fracture spacing between massive to thick-bedded shelf-margin (~17 m fracture spacing) and outer-shelf facies tracts versus thin-bedded outer-shelf and shelf-crest (~28 m fracture spacing). Ultimately, this study demonstrated that the Capitan shelf margin was ubiquitously overprinted by syndepositional fracturing and faulting and that this nearsurface structural modification influenced early diagenetic patterns and internal vii sedimentation throughout the reef margin. Before this study, the extent and nature of syndepositional fracture/fault development within the margin were largely unquantified. Here, by integrating field observations and surface weathering reflections of these fractures as observed in the lidar, we can demonstrate a widespread impact of early fracturing more akin to analogous early-lithified margins such as the Devonian of the Canning Basin of Australia. / text

The Mural Limestone, located in the Mule Mountains to the northeast and southeast of Bisbee, Arizona provides an exceptional outcrop analog for time-equivalent productive reservoirs in the Albian Glen Rose patch-reef play of the Maverick Basin. The Mural Limestone is exposed in a number of folds and east-dipping fault blocks in the Grassy Hill and Paul Spur localities in the Mule Mountains and represents a remnant of a south-facing distally-steepened carbonate ramp that prograded into the Chihuahua Trough in Albian time. This study documents the detailed facies architecture and sequence stratigraphic setting of a multicyclic patch-reef and its associated ramp interior facies at the Paul Spur and Grassy Hill localities, respectively. Small mud-dominated coral-algal buildups (~5 m thick) and tabular biostromes (up to 1.5 m thick) consisting of rudist floatstones are common in the bedded ramp interior carbonates at the Grassy Hill locality in the Mule Mountains 10 km landward of the Paul Spur reef. Buildups in this area are flanked by weakly-cyclic and well-bedded skeletal mud- and grain-dominated packstones. At the Paul Spur locality, Mural facies consist of a 10-35 m thick patch-reef with four distinct reef communities: microbial-Microsolena framestone, algal-Actinastrea boundstone, branching coral-skeletal framestone and caprinid-requienid floatstone. Measured reef dimensions show a distinct windward-leeward margin with reef frame facies extending ~70 m from the margin and extensive leeward rudstone debris and grainstone shoal facies extending a distance of 870 m. Reef and backreef shoal facies exhibit low preserved porosity but petrographic analysis of backreef grainstones shows that primary porosity and permeability was present. These extensive reservoir-prone shoals may be a suitable reservoir target similar to flank rudstones and grainstones of the Maverick Basin reefs. Three aggradational to retrogradational cycles of reef growth are evident at the Paul Spur locality. Retrogradational stacking is consistent with that of time-equivalent Lower Glen Rose patch-reefs in the Maverick Basin of Texas, which suggests a eustatic driver for stratigraphic architecture along the Bisbee/Comanche shelf. Backstepping of reef frame facies in Cycle 3 is interpreted to be time-equivalent to patch-reef development at the Grassy Hill locality. / text

No description available.

Marine protected areas (MPAs) have been established along the East African coast to protect coral communities from human and natural disturbance. Their success is dependent on the degree to which resource populations are self-seeding or otherwise connected. Estimates of contemporary gene flow on or between south-east African reefs are thus required to reveal the interdependence of the South African coral communities and those to the north. Accordingly, the ecologically relevant (1 or 2 generations) connectivity of two broadcast-spawning corals, Acropora austera and Platygyra daedalea, was assessed on reefs in the region, from the Chagos Archipelago to Bazaruto Island in Mozambique and Sodwana Bay in South Africa, using hyper-variable genetic markers. Analysis of genetic diversity and differentiation provided evidence for the existence of four discrete genetic populations of A. austera and five of P. daedalea in the sampled area. Higher genetic diversity was found on northern South African reefs (Nine-mile Reef and Rabbit Rock) and migration patterns inferred from assignment tests suggested that, at ecological time scales, South African reefs are disconnected from those in Mozambique and might originate from a source of gene flow that was not sampled. The analysis of fine-scale genetic connectivity conducted on Two-mile Reef (TMR) demonstrated the existence of significant spatial genetic structure at the reefal scale that might be related to the non-random dispersal of coral larvae, putatively explaining the genetic discontinuity observed in the region. Altogether, the results are consistent with the isolation observed in other studies using less variable markers, and support the hypothesis that there is demographic discontinuity between the coral populations along the south-east African coast. More importantly, Acropora austera and P. daedalea represent different life strategies in the South African reef communities yet manifested similar genetic patterns, suggesting that these corals are responding similarly to forces that are driving genetic connectivity in the region. For management purposes, the genetically distinct populations identified at each of the spatial scales analysed in this study may correspond to management units, or evolutionarily significant units. Furthermore, since some reefs appear to act as “landing-sites” for migrants (Nine-mile Reef) and there is evidence of significant within-reef genetic structure (TMR), an adaptive management framework would be the best option for the MPA in the region. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2014.

People are active participants in coral reef ecosystems. This ethnobiology study considers and contrasts folkbiological knowledge of people living in two groups of artisanal fishing villages in Kadavu Province, Fiji. The high level of biological diversity on the Astrolabe Reef provides insights into folk categorization and classification methods that include colour, shape, size, physical features, and habits of certain reef fish and marine animals. Surveying large numbers of experts and novices on defined groups of creatures yields more depth and range of responses allowing higher confidence levels in response accuracy. A comparison of the data with Berlins (1992) proposed principles yields mixed results. Sea cucumbers have high ecological salience and their identification requires attention to the affect of two centuries of trade on Fijian society. Effective ethnobiological research provides productive options to contribute to coral reef sustainability programs with long term benefits for local people and marine life. Key words: Kadavu, naming and classification of fish, coral reef ethnobiology.

Thesis (M.A.)--University of Hawaii at Manoa, 2004. / Includes bibliographical references (leaves 74-82). / xi, 82 leaves, bound ill., maps 29 cm

Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra�ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota. There were four major habitat types (rubble/rock, sand/coral matrix, algal rim and sand) identified, the most extensive being rubble/rock (45%) and sand/coral matrix (35%). The degree of exposure to winds was found to correlate with the reef development and habitat distribution. The assemblage composition of each major habitat type differed significantly from every other habitat. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity, and the highest number of species and individuals. The overall abundance of the fauna was dominated by holothurians (68%) and echinoids (30%), while Trochus niloticus and Tridacna maxima accounted for the remaining 2% of the total invertebrate assemblage. Clear habitat partitioning was also found for adult and juvenile Trochus niloticus and Tridacna maxima. In the traditional fishery for Holothuria leucospilota, the mature gonads of males are harvested by making an incision in the body-wall of the animal, removing the gonads and then returning the animal to the reef to allow regeneration. Monthly collections of H. leucospilota were used to describe the reproductive biology of this species. Gametogenesis and spawning were synchronous between the sexes and spawning occurred annually during summer, when water temperature and photoperiod were at their highest. Although the incision in the body-wall and gonad removal had no impact on the survival of H.leucospilota in experimental cages, their body weight, and general sheltering and feeding behaviors were affected. Gonads took at least 41 days to start regenerating, suggesting a considerable delay in the spawning of fished individuals. In 1998, five Rarotongan communities re-introduced the traditional ra�ui system of resource management, prohibiting all fishing and gathering from their reefs. The performance of the Nikao ra�ui, which had been put in place to allow trochus stocks to increase, was investigated. Comparisons of macroinvertebrate assemblage composition and species density were made between three fishing treatments, i.e. fished areas adjacent to the ra�ui, within the ra�ui after two years of protection, and in the ra�ui after it had been lifted for three weeks to allow a commercial trochus harvest. Analysis of variance on the count data for the twelve most abundant species, and non-metric multi-dimensional scaling indicated that there were no differences in the microhabitat or the invertebrate assemblage composition between the three fishing treatments. However, there were significant differences between the rubble/rock and sand/coral matrix habitat types. The results on the effectiveness of the Nikao ra�ui are equivocal, due to the small sample size, and the variability between samples which was highlighted by the wide confidence intervals. This study highlights the importance of habitat to the macroinvertebrate fauna of the reef-top and the need for accurate habitat maps to increase the cost-effectiveness of future resource surveys, to provide information to management, and for the design of Marine Protected Areas. The mapping and survey methods must be reliable and repeatable in terms of the limitations of time, and the availability of expertise, funding and resources. The results provide important information for fisheries and conservation managers of Rarotonga and other Pacific Islands to better design rigorous sampling programmes for monitoring the status of reef-top resources, and for evaluating and planning Marine Protected Areas.

[Truncated abstract] Selection of priority areas for Marine Park conservation is often compromised by the lack of comprehensive biodiversity data and the resources and expertise necessary to gain this information directly by sampling. One cost effective alternative is the use of species groups or indicator species as surrogates for total biodiversity. However use of these surrogates requires an ecological understanding of how they reflect biodiversity gradients. A framework for unravelling these relationships has been suggested that involves relating species biodiversity to different and competing ecological models using appropriate statistical analysis. I use this framework to explore coral species biodiversity over a range of environmental gradients encompassing the North West Shelf of Australia and the Great Barrier Reef in North East Australia. ... I assessed physiological responses of corals to physical factors to corroborate crossshelf patterns in species biodiversity. Finally, I investigated to what extent coral cooccurrence based species groups (or guilds) can be used as surrogates for total coral biodiversity. The major findings of this thesis were: i) coral biodiversity along cross-shelf environments was highly correlated to specific gradients of abiotic reef conditions; ii) larval modelling indicates the potential for significant connectivity across continentalshelf environments such that differences in species distribution are not simply as a result of self seeding. iii) similar correlative patterns were demonstrated for coral species that occur along comparable abiotic gradients in reef areas of both Eastern and Western Australia, suggesting a causal relationship between the physical environment and coral biodiversity; iv) coral physiological parameters measured using lipid fractions independently corroborated the hypothesis that there is a biological basis for observed coral distributions; v) reef coral communities are not highly structured across abiotic physical gradients and biodiversity across the shelf increases as conditions become suitable for a wider range of species; vi) total coral biodiversity can be estimated very accurately (within r2 values ranging from 0.75 to 0.90) using a small number (15-30) of optimally chosen indictor species using the randomForest statistical method. These results suggest coral biodiversity over cross-shelf environments conforms most closely to the